miRWalk citations :

About miRWalk2.0

miRWalk2.0
is an improved version of the previous database (i.e. miRWalk). miRWalk2.0 is so far the only freely accessible,
comprehensive archive, supplying the biggest available collection of predicted and experimentally verified miRNA-target interactions
with various novel and unique features (missing in a previous version i.e. miRWalk) to greatly assist the miRNA research community.

It hosts possible binding site interaction information (including "central pairing sites")
between genes (encompassing the complete sequence as well as mitochondrial genomes) and
miRNAs resulting from the miRWalk algorithm by walking with a heptamer (7nts)
seed of miRNA from positions 1 to 6.
These different starting positions are considered because
it has recently been identified that miRNAs also regulate the expression of their target genes
by annealing from nucleotides 4 to 15 (PMID:20620952).

A comparative platform of miRNA binding sites on mitochondrial genomes is also integrated.

Recently, it has been suggested that miRNAs can also base-pair with other miRNAs (PMID:14730015).
Therefore, miRWalk2.0 not only offers miRNA-miRNA interactions,
but also combines this information with a comparison of binding sites resulting from 4 prediction algorithms: miRanda, PITA, RNAhybrid and Targetscan.

A comprehensive atlas is implemented to supply a comparative overview of human homologous genes,
their classes, pathways and ontologies among 15 species.

One can also obtain miRNAs which are significantly enriched for their binding sites within the genes associated with pathways, ontologies and classes.

To foster large-scale enrichment analysis, a novel feature named “Customized datasets” is
implemented through which users can generate a customized list of putative targets on their
miRNAs of interest from 13 different data-sets for promoter, CDS, 5’- and/or 3’-UTR regions.

It provides genomic location search functionality for genes to determine which of miRNA(s) share
the same or nearby location – as previous studies suggest that several mammalian miRNA genes are
co-expressed with their host-gene and/or neighboring genes by utilizing their transcriptional machinery
and promote synergistic and/or antagonistic effects on them (PMID:20370903).

The web-interface of miRWalk2.0 is broadly classified into the Predicted Target (PTM) and the Validated Target (VTM) modules.These two modules are further categorized into different search pages, allowing users to fetch miRNA associated information using different identifiers.

The Predicted Target module hosts miRNA-target interactions information within the complete sequence of
all known genes of human, mouse and rat including all transcripts and mitochondrial genomes.
It also provides novel comparative platforms of miRNA binding sites resulting from 13 data-sets for promoter, cds, 5'-, and 3'-UTR, mitochondrial genes and
miRNA-miRNA interactions. miRBase release 20 is utilized to generated miRNA-target interaction information for this module.

The Validated Target module hosts experimentally verified miRNA interaction information associated with genes, pathways, organs, diseases,
cell lines, OMIM disorders and literature on miRNAs. This module is last updated on 29th September 2014.
In addition, it provides the information on proteins known to be involved in miRNA processing.